Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020745.1 Corchorus olitorius cultivar O-4 contig20778, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17640
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:4705 original size:60 final size:60
Alignment explanation
Indices: 4637--4801 Score: 199
Period size: 60 Copynumber: 2.8 Consensus size: 60
4627 GCTAATTGCT
* * *
4637 CAAATAAGGGTCTAACATT-TGCCAAAATGCTCAAATAAGGGCCTGATGTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTAT-CAAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
* **
4697 CAAATAAGGGTCTAACGTTATCAAAAATGTTCAAATAA-GGATTCGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTATCAAAAATGCTCAAATAAGGGCCT-GATCTTTTAATTTGGC
* * * * *
4757 CAAATAAGTGCCTAACGTTATCGAAAATGCTCAGATAAGAGCCTG
1 CAAATAAGGGTCTAACGTTATCAAAAATGCTCAAATAAGGGCCTG
4802 GCGTCGAAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 3 0.03
60 82 0.93
61 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGTCTAACGTTATCAAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:4942 original size:60 final size:60
Alignment explanation
Indices: 4840--4956 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
4830 ACTGACACCA
* * * * *
4840 GGCCCTTATTTGAGCATTTTTGATAACGTTAGACCCTTATTTGACTAAATTAAAAGACCG
1 GGCCCTTATATGAACATTTTCGATAACGTTAGACCCTAATTTGACCAAATTAAAAGACCG
*
4900 GGCCCTTATATGAACATTTTCGATAACGTTAGGCCCTAATTTGACCAAATTAAAAGA
1 GGCCCTTATATGAACATTTTCGATAACGTTAGACCCTAATTTGACCAAATTAAAAGA
4957 TCAGACCCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (60 bp):
GGCCCTTATATGAACATTTTCGATAACGTTAGACCCTAATTTGACCAAATTAAAAGACCG
Found at i:4966 original size:60 final size:60
Alignment explanation
Indices: 4836--4968 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 60
4826 CCAAACTGAC
* * * * * *
4836 ACCAGGCCCTTATTTGAGCATTTTTGATAACGTTAGACCCTTATTTGACTAAATTAAAAG
1 ACCAGACCCTTATATGAACATTTTCGATAACGTTAGACCCTAATTTGACCAAATTAAAAG
* * *
4896 ACCGGGCCCTTATATGAACATTTTCGATAACGTTAGGCCCTAATTTGACCAAATTAAAAG
1 ACCAGACCCTTATATGAACATTTTCGATAACGTTAGACCCTAATTTGACCAAATTAAAAG
*
4956 ATCAGACCCTTAT
1 ACCAGACCCTTAT
4969 TTAAGTATTA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (60 bp):
ACCAGACCCTTATATGAACATTTTCGATAACGTTAGACCCTAATTTGACCAAATTAAAAG
Found at i:5229 original size:60 final size:62
Alignment explanation
Indices: 5118--5232 Score: 207
Period size: 60 Copynumber: 1.9 Consensus size: 62
5108 AACTATCATC
5118 ATATACGTAAGATTAAATAAATAAAAAATTTAAGTCATTATCTTGTCAACATTAGGTAGCAA
1 ATATACGTAAGATTAAATAAATAAAAAATTTAAGTCATTATCTTGTCAACATTAGGTAGCAA
*
5180 ATATACGTAAGATTAAATAAAT-ATAAA-TTAAGTCATTATCTTGTCAACATTAG
1 ATATACGTAAGATTAAATAAATAAAAAATTTAAGTCATTATCTTGTCAACATTAG
5233 TTAACCAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
60 26 0.50
61 4 0.08
62 22 0.42
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (62 bp):
ATATACGTAAGATTAAATAAATAAAAAATTTAAGTCATTATCTTGTCAACATTAGGTAGCAA
Found at i:5246 original size:62 final size:62
Alignment explanation
Indices: 5118--5246 Score: 199
Period size: 60 Copynumber: 2.1 Consensus size: 62
5108 AACTATCATC
*
5118 ATATACGTAAGATTAAATAAATAAAAAATTTAAGTCATTATCTTGTCAACATTAGGTAGCAA
1 ATATACGTAAGATTAAATAAATAAAAAATTTAAGTCATTATCTTGTCAACATTAGGTACCAA
* *
5180 ATATACGTAAGATTAAATAAAT-ATAAA-TTAAGTCATTATCTTGTCAACATTAGTTAACCAA
1 ATATACGTAAGATTAAATAAATAAAAAATTTAAGTCATTATCTTGTCAACATTAGGT-ACCAA
5241 TATATA
1 -ATATA
5247 TATAATTCAT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
60 27 0.44
61 8 0.13
62 27 0.44
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (62 bp):
ATATACGTAAGATTAAATAAATAAAAAATTTAAGTCATTATCTTGTCAACATTAGGTACCAA
Found at i:13778 original size:9 final size:9
Alignment explanation
Indices: 13766--13813 Score: 60
Period size: 9 Copynumber: 5.0 Consensus size: 9
13756 CTAAATGCCT
13766 CAAATCTCC
1 CAAATCTCC
13775 CAAATCTCC
1 CAAATCTCC
13784 CAAATCTCC
1 CAAATCTCC
13793 CATATTATCTCC
1 CA-A--ATCTCC
*
13805 CAAAACTCC
1 CAAATCTCC
13814 ACGAAACCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
9 25 0.71
10 1 0.03
11 1 0.03
12 8 0.23
ACGTcount: A:0.33, C:0.42, G:0.00, T:0.25
Consensus pattern (9 bp):
CAAATCTCC
Found at i:13804 original size:21 final size:18
Alignment explanation
Indices: 13766--13813 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 18
13756 CTAAATGCCT
13766 CAAATCTCCCAAATCTCC
1 CAAATCTCCCAAATCTCC
13784 CAAATCTCCCATATTATCTCC
1 CAAATCTCCCA-A--ATCTCC
*
13805 CAAAACTCC
1 CAAATCTCC
13814 ACGAAACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.42
19 1 0.04
21 14 0.54
ACGTcount: A:0.33, C:0.42, G:0.00, T:0.25
Consensus pattern (18 bp):
CAAATCTCCCAAATCTCC
Done.